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New Zealand's freshwater fish species are in peril - and especially in our pastoral countryside, researchers say.

In a study published today, Victoria University's Dr Mike Joy and colleagues compared land use changes and more than 20,000 freshwater fish records since 1970.

The data, which covered fish distribution and abundance trends, along with a key measure of water pollution called the Index of Biotic Integrity (IBI), showed more than three quarters of 25 analysed species were in decline.

About the same rate of decline was found in 20 native fish species - and in two thirds of cases, the drop was a significant one.

"We've gone from one species out of every five being in trouble to a situation where three species out of four are staring extinction in the face, and we've done it in one generation."

Given the study's findings, he said, it was "bizarre" that there was little protection for native fish.

"And the fact that despite these declines and developed world's worst proportion of threatened species we harvest them, the Department of Conservation [DoC] doesn't protect them."

Joy acknowledged a just-announced amendment to the Conservation Act aimed at native freshwater fish, but added this only covered protected areas.

"They have to get there first, through the polluted unprotected rivers."

He was also sceptical of new guidelines around structures built in rivers and streams that could impede migrating fish, criticising them as guidelines only.

"Under the Freshwater Fisheries Act 1983, it is clearly stated it is illegal to block native fish passage - but there have been thousands of barriers put in since then and DoC has to my knowledge never used their powers under this act to do anything."

"We've been trying to have our cake and eat it - we need to stop or soon there won't even be crumbs left," Victoria University's Dr Mike Joy says. Photo / File

Tackling the decline of fish, he argued, could only be done by addressing wider issues facing our rivers, streams and lakes.

"We need to match land use to soil types and slopes to control runoff, we need major reductions in intensity, and we need to look hard at the way local councils are charged with protecting both the economy and the environment when they apply the Resource Management Act - and yet somehow always end up letting the economy win," he said.

"We've been trying to have our cake and eat it. We need to stop or soon there won't even be crumbs left."

The Government was working on new bottom-line rules for regional councils that would remove farming intensity as a "permitted activity" and set tougher levels for nutrients.